model library clean up

[stevencarlislewalker]

• make one example that is 'perfect'
• all models have Rmd README files so that we can show basic simulations and flow diagrams for all models
• comment throughout and link to package reference https://canmod.github.io/macpan2/reference/index.html and vignetteshttps://canmod.github.io/macpan2/articles/index.html throughout
• start all example models with installation and dependency info
• decide what to do linking to other models not in the tmb.R/calibration_example.R/README.[R]md format (e.g., https://phac-nml-phrsd.github.io/EPACmodel/, which is linked to in the main package readme but not as a model in the library).
• add a folder sister to starter_models that contains lists of example usage
• add an age/geographic model -- decide how to deal with the fact that we still do not have good model structure functionality
• add additional flows suggested by david c for ww
• add vector-borne model (https://homepages.warwick.ac.uk/~masfz/ModelingInfectiousDiseases/Chapter4/Program_4.4/index.html) (need to decide what to do with absolute birth rates) -- decision: just use per-capita birth
• convert all flows to explicit flows. for example, this and this and this are good but this is not good because it uses the formula notation still within the mp_per_capita_flow function and this is not good because it does not even use mp_per_capita_flow and friends.